Annual Scientific Report 2015

Marioni group
• Improved and extended models for finding heterogeneously
expressed genes using scRNA-sequencing;
• Used scRNA-seq to characterise the first cell fate decisions in
the early embryo;
• Applied scRNA-seq to study heterogeneity in embryonic
stem cells.
Saez-Rodriguez group
• Identified biomarkers of drug efficacy in cancer cell lines
from multiple types of data: genomic, epigenomic and
transcriptomic;
• Completed analysis of collaborative competitions (DREAM
challenges), assessing the state of the art of prediction of
drug toxicity and of inference of signalling networks in
cancer cells;
• Developed a method to reconstruct signalling pathways from
mass-spectrometry phospho-proteomic data, and applied it
to the study of breast cancer.
Stegle group
• Developed advanced statistical fast models to test genetic
effects across multiple phenotypes in populations;
• Surveyed the regulatory effect of structural variants in the
context of the 1000 Genomes Project;
• Devised integrative analytical strategies to investigate
interaction effects between multiple genetic variants and
environmental factors;
• Developed one of the first statistical approaches to account
for confounding factors in single-cell transcriptome
sequencing studies;
• In applications to T-cell differentiation studies, we find
that this method reveals otherwise masked subpopulations
of cells.
‘Periodic Table’ of protein complexes, providing a predictive
framework for anticipating new, unobserved topologies of
protein complexes;
• Developed a computational pipeline that provides a generic
approach for processing scRNA-seq data and removing
low-quality cells, ensuring that only correctly annotated cells
are included in downstream analyses.
Thornton group
• Expanded understanding of the biochemistry and diversity
of isomerisation by creating a robust method for comparison
and clustering of isomerase reactions into classes;
• Studied enzyme function within 379 protein domain
superfamilies, and provided insights useful for predicting the
function of uncharacterised sequences and in the design of
new synthetic enzymes;
• Conducted a genome-wide association study of Drosophila
lifespan, and found that the top associated genes provide
good candidates for further investigation into their
relationship with lifespan and ageing;
• In collaboration with the Institute of Healthy Ageing at
UCL, tested the effect of manipulating 10 of the genes most
significantly associated with lifespan;
• In a combined computational–experimental study,
presented the first confirmed example of a plant-pollen-like
protein in a worm that is targeted by IgE, addressing an
important question in allergy and parasitology.
Teichmann group
• Investigated the transcriptome profiles of mESCs in
three different culture conditions representing different
pluripotent states, and revealed additional pluripotency
network genes, including Ptma and Zfp640;
• Developed a novel computational method, TraCeR, that links
TCR sequence with transcriptional profiles in individual
cells with high accuracy and sensitivity;
• Using mass spectrometry data and a large-scale analysis
of structures of protein complexes, identified repeating
patterns in the assembly transitions and created a new
2015 EMBL-EBI Annual Scientific Report 37